Update:
I've just been through a ticket with SM and have gained a bit more knowledge on the way the spam filters and content filters are working.
The reason the content filters aren't working is more than likley because the spam filters are working better and if they trigger first, it won't look to the content filters to do anything as it's already been filtered.
I think i've seen this because my spam filters are actually working better now and placing everything in the spam folder instead of it getting to my content filters that removed the emails or placed them in specific folders.
So, 2 options really.
1) Leave the filtering to do its work and if they are all spam going into the spam folder, choose what you do with them with the main spam filters, whether it be delete or just move to spam.
2) Change your weight ranges so certain probablility of spams don't get moved into spam, then these emails will then go onto the domain level spam filters and if not picked up by them, then onto the content filters.
I'm going to have a play around with the weight ranges and see what happens and when it starts triggering the content filters.
Spam/Content filter order:
1) System Spam checks
2) Domain level Spam checks (if different)
3) Domain level Content Filters
4) User level Spam checks (if different)
5) User level Content Filters